GRID map

Besides the aforementioned descriptors, grid-based methods are frequently used in the field of QSAR quantitative structure-activity relationships) [50]. A molecule is placed in a box and for an orthogonal grid of points the interaction energy values between this molecule and another small molecule, such as water, are calculated. The grid map thus obtained characterizes the molecular shape, charge distribution, and hydrophobicity. 

To produce this kind of grid map by quickly measuring the concentrations at some points for immediate processing and graphical presentation is a simple and often effective way to communicate the results to persons w ho are not trained to analyze primary results of measurements. The method must, however, be used with care since there is a risk that the sampling of data itself may affect the airflow in the studied area. I he equipment needed is relatively expensive, and the method is therefore of interest when the prerequisites are already available for other reasons. 

It is of course also possible to arrange so that the measurements are made at every point with a fixed instrument and the data transferred to a computer equipped with suitable software to produce the grid map, all in real time. If the graph is also superimposed on a video picture from the measured area, the result will be a video, visualizing the. spatial distribution in real time. 

The author would like to acknowledge Peter Colman, my collaborator in neuraminidase crystallography, Mike Lawrence for the GRID maps shown here and reading this manuscript, Brian Smith for discussions on enzyme mechanisms, Jenny McKimm-Breschkin for discussions on drug resistance, Bert van Donkelaar for technical support, and Paul Davis for computing support. 

The GPF is used to calculate the grid maps (the -1 option specifying the grid logfile [GLG]) ... 

Fig. 8. (Opposite page) Example of grid parameter file for use in AutoDock. The file is largely self-explanatory. Reference is made to the grid maps that have been calculated using different molecular entities to probe the interaction with the protein.

Make a copy of the sampling grid map from the SAP and use it in the field for recording of actual measurements and sampling points. 

If the SAP does not contain the grid maps, make accurate drawings of the sampled areas and document the exact positions of the sampling points. 

Cruciani G, Crivori P, Carrupt PA, Testa B (2000) Molecular fields in quantitative structure-permeation relationships The VolSurf approach. Theochem 503 17-30 Cruciani G, Pastor M, Clementi S (2000) Handling information from 3D GRID maps for QSAR studies. In Gun-dertofte K, Jorgensen FS (eds) Molecular modelling and prediction of bioactivity, proceedings of the 12th European symposium on quantitative structure-activity relationships (QSAR 98). Plenum Press, New York, pp 73-81 Cruciani G, Pastor M, Guba W (2000) VolSurf A new tool for the pharmacokinetic optimization of lead compounds. Eur J Pharm Sd 11 S29-S39... 

To prepare GRID maps which are intuitively easy to understand, and can therefore provide a focal point for discussions between people with backgrounds in different fields of science, and indeed for people with little formal scientific training. 

This article is not the place in which to consider statistical methods in detail, but the use of GRID maps to interpret interesting features of molecular structures will now be described. 

This GRID map is therefore misleading, and this figure demonstrates how important it is to use MIF programs with great care because it is very easy to obtain deceptive results by misusing any MIF program. See text. 

Figure 1.9. A molecule of leucine with GRID maps for a hydrophobic probe (A, yellow) a multiatom cis-amide probe (B, red) and an sp3 NHj probe (C, blue). See text.

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